Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome
Niranjan Nagarajan
时长：18:51
分会场：2019中国肠道大会 - 新技术大会
The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing. The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9× long read coverage, thus enabling high quality assembly of lowly abundant species (80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences.
Niranjan Nagarajan
新加坡基因组研究院计算与系统生物学中心
"Senior Group Leader
Associate Director, Computational and Systems Biology
Professor Nagarajan and his team's research primarily focuses on developing novel statistical and combinatorial algorithms to analyse massive genomic datasets and provide biological insights. A defining aspect of their computational genomics work is the use of parametric complexity analysis and exact algorithms to design bioinformatics tools with provable performance guarantees. They primarily focus on addressing questions in three areas a) Sequence Analysis & Assembly b) Metagenomic Analysis and c) Integrative Genomics. "
